Showing papers by "Laboratory of Molecular Biology published in 1987"
TL;DR: The results suggest that the protein has a role in the normal secretion of metabolites and certain anti-cancer drugs into bile, urine, and directly into the lumen of the gastrointestinal tract.
Abstract: Monoclonal antibody MRK16 was used to determine the location of P-glycoprotein, the product of the multidrug-resistance gene (MDR1), in normal human tissues. The protein was found to be concentrated in a small number of specific sites. Most tissues examined revealed very little P-glycoprotein. However, certain cell types in liver, pancreas, kidney, colon, and jejunum showed specific localization of P-glycoprotein. In liver, P-glycoprotein was found exclusively on the biliary canalicular front of hepatocytes and on the apical surface of epithelial cells in small biliary ductules. In pancreas, P-glycoprotein was found on the apical surface of the epithelial cells of small ductules but not larger pancreatic ducts. In kidney, P-glycoprotein was found concentrated on the apical surface of epithelial cells of the proximal tubules. Colon and jejunum both showed high levels of P-glycoprotein on the apical surfaces of superficial columnar epithelial cells. Adrenal gland showed high levels of P-glycoprotein diffusely distributed on the surface of cells in both the cortex and medulla. These results suggest that the protein has a role in the normal secretion of metabolites and certain anti-cancer drugs into bile, urine, and directly into the lumen of the gastrointestinal tract.
2,757 citations
TL;DR: The relatively few residues that, through their packing, hydrogen bonding or the ability to assume unusual phi, psi or omega conformations, are primarily responsible for the main-chain conformations of the hypervariable regions are identified.
2,400 citations
TL;DR: It is proposed that the KDEL sequence marks proteins that are to be retained in the ER and discuss possible retention mechanisms.
2,127 citations
TL;DR: The extent to which groups of residues (charged, polar and non-polar) are buried within proteins correlates well with their hydrophobicity derived from amino acid transfer experiments, and an effective coefficient of partition for each type of residue is calculated and compared with other sets of partition coefficients derived directly from experimental data.
910 citations
TL;DR: The crystal structure of a B-type DNA dodecamer containing a homopolymeric run of six A·T base pairs shows that this region possesses special structural features, including a system of bifurcated hydrogen bonds, which explains some of the properties of this simple homopolymer.
Abstract: Poly(dA).poly(dT) has unusual properties in that it cannot associate into nucleosomes and short, phased runs of it cause DNA bending. The crystal structure of a B-type DNA dodecamer containing a homopolymeric run of six A.T base pairs shows that this region possesses special structural features, including a system of bifurcated hydrogen bonds, which explains some of the properties of this simple homopolymer.
893 citations
TL;DR: This work describes how a parallel analogue algorithm, derived from a formal model for the establishment of topographically ordered projections in the brain, can be applied to the travelling salesman problem, and produces shorter tour lengths than another recent parallel analogue algorithms.
Abstract: The travelling salesman problem is a classical problem in the field of combinatorial optimization, concerned with efficient methods for maximizing or minimizing a function of many independent variables. Given the positions of N cities, which in the simplest case lie in the plane, what is the shortest closed tour in which each city can be visited once? We describe how a parallel analogue algorithm, derived from a formal model for the establishment of topographically ordered projections in the brain, can be applied to the travelling salesman problem. Using an iterative procedure, a circular closed path is gradually elongated non-uniformly until it eventually passes sufficiently near to all the cities to define a tour. This produces shorter tour lengths than another recent parallel analogue algorithm, scales well with the size of the problem, and is naturally extendable to a large class of optimization problems involving topographic mappings between geometrical structures.
833 citations
TL;DR: Putative Zn fingers are present in different numbers within the structure of many regulatory proteins and serve as modules for the building up of a specific nucleic acid binding domain.
643 citations
TL;DR: The halltnark of the immune response is its specificity and the specificity is directly correlated with the affinity of the antigen-antibody interaction, which means that T cells may not have developed the equivalent of the elaborate mechanism which is the object of this paper.
Abstract: The halltnark of the immune response is its specificity and the specificity is directly correlated with the affinity of the antigen-antibody interaction. The requirement for high affinity antibodies may be more important than specificity alone, since antibodies are designed to detect soluble antigens which are sometimes capable of inflicting great harm at very low concentrations (e.g. toxins). This may not be required by. or may even be a disadvantage to T-cell responses where the affinity for the ligand involves interactions of the T-cell receptor not only with antigen, but also with other molecules, e.g. those involved in MHC restriction (Yague et al. 1985. Dembic et al. 1986). T cells therefore may not have developed the equivalent of the elaborate mechanism which is the object of this paper. During the course of an antigen-specific immune response, the affinity of the serum increases with time, a phenomenon commonly referred to as maturation of the response (Jerne 1951, Siskind & Benaceraff 1969). Such a maturation results from specific alterations of the structure of the antibody molecules (Steiner & Eisen 1967). What is the precise nature of these alterations, which are the root of the production of high affinity antibodies? There is no doubt that somatic mutation contributes to antibody diversity (Weigert et al. 1970. Bernard et al. 1978, Griffiths et al. 1984). There are many reasons to believe that a mechanism of hypermutation operates within restricted stretches of the DNA to further diversify the genes encoding the antibody molecules (Kim et al. 1981, Gearhart & Bogenhagen 1983). This mutational drift is, however, not the full extent of the change. Major changes in the antibody structures involved result from a shift in the antigen-specific B-cell repertoire over the course of the immune response. In the primary response the most frequent B-cell clones already expressing antibody molecules with a relatively
624 citations
TL;DR: The backbone structure of the antigen, lysozyme, is mostly unperturbed, although there are some changes in the epitope region, most notably Pro-70, and the Fab elbow bends in the two crystal forms differ by 7 degrees.
Abstract: We have determined the three-dimensional structure of two crystal forms of an antilysozyme Fab-lysozyme complex by x-ray crystallography. The epitope on lysozyme consists of three sequentially separated subsites, including one long, nearly continuous, site from Gln-41 through Tyr-53 and one from Gly-67 through Pro-70. Antibody residues interacting with lysozyme occur in each of the six complementarity-determining regions and also include one framework residue. Arg-45 and Arg-68 form a ridge on the surface of lysozyme, which binds in a groove on the antibody surface. Otherwise the surface of interaction between the two proteins is relatively flat, although it curls at the edges. The surface of interaction is approximately 26 X 19 A. No water molecules are found in the interface. The positive charge on the two arginines is complemented by the negative charge of Glu-35 and Glu-50 from the heavy chain of the antibody. The backbone structure of the antigen, lysozyme, is mostly unperturbed, although there are some changes in the epitope region, most notably Pro-70. One side chain not in the epitope, Trp-63, undergoes a rotation of approximately 180 degrees about the C beta--C gamma bond. The Fab elbow bends in the two crystal forms differ by 7 degrees.
586 citations
TL;DR: The purification of RAP1 by DNA affinity chromatography and the isolation of its gene from a lambda gt11 genomic library using antibodies raised against the protein suggest that R AP1 may be a transcriptional regulator that can play a role in either repression or activation of transcription, depending upon the context of its binding site.
552 citations
TL;DR: A novel gene of the calmodulin superfamily, encoding a 29-kD neuronal protein here named "calretinin," has been isolated as a cDNA clone from chick retina, and RNAs from both genes are abundant in the retina and in many areas of the brain, but calretin in RNA is absent from intestine and other nonneural tissues.
Abstract: A novel gene of the calmodulin superfamily, encoding a 29-kD neuronal protein here named "calretinin," has been isolated as a cDNA clone from chick retina. The encoded sequence includes four putative calcium-binding sites and a fusion protein binds calcium. The most similar protein known is the 28-kD intestinal calcium-binding protein, calbindin (58% homology). Both genes date from before the divergence of chicks from mammals. The distribution of calretinin and calbindin mRNAs in chick tissues has been mapped using RNA gel blots and in situ hybridization. RNAs from both genes are abundant in the retina and in many areas of the brain, but calretinin RNA is absent from intestine and other nonneural tissues. Calretinin and calbindin are expressed in different sets of neurons throughout the brain. Calretinin RNA is particularly abundant in auditory neurons with precisely timed discharges.
TL;DR: The nature and exact extent of the sequence variations and the extent to which the conserved features of the globin sequences are unique to this family are determined.
TL;DR: The multiple alignment algorithm yields an assignment of disulphide connectivity in mammalian serotransferrin that is consistent with crystallographic data, whereas pairwise alignments give an alternative assignment.
TL;DR: Toxin lacking domain Ia is about 100-fold less toxic to mice than intact PE and should be a useful molecule for the construction of immunotoxins.
TL;DR: It is suggested that the AS-C encodes several homologous polypeptides, which represent a subset of a larger gene family, and each member of the family functions at an equivalent stage of a unique morphogenetic operation involving the segregation of individual neural lineages from the epidermal anlage.
TL;DR: From the sequence conservation and the predicted secondary structure, many active site regions of enzymes can be located and the entire algorithm is fully automatic and is applicable to all structural classes of globular proteins.
TL;DR: The cloning of sequences from a segment‐polarity gene, wingless, and the in situ localization of a transcript in embryos are described, which discusses the pattern of expression with respect to models of pattern formation in segmental units.
Abstract: In Drosophila the process of segmentation depends on the function of coordinate, gap, pair-rule and segment-polarity genes. Mutations in segment-polarity genes cause defects in the pattern of every segment. Here the cloning of sequences from a segment-polarity gene, wingless, and the in situ localization of a transcript in embryos are described. The transcript is first detected in the anterior and posterior regions of the blastoderm embryo at cellularization, and accumulates in a series of stripes in the extended germ band, one stripe per metameric unit. Each stripe is localized to the most posterior cells of each parasegment. The signal is predominantly epidermal, and transcript accumulates only transiently in the mesoderm and nervous system. This pattern of expression is discussed with respect to models of pattern formation in segmental units.
TL;DR: The yeast heat-shock factor binds constitutively to DNA but only activates transcription after heat-induced phosphorylation, and the mobility of protein-HSE complexes on polyacrylamide gels is altered following heat shock.
Abstract: When cells are exposed to elevated temperatures, transcription of a small set of genes, the heat-shock genes, is activated. This response is mediated by a short DNA sequence, the heat-shock element (HSE), which is thought to be the binding site for a specific transcription factor. Studies with Drosophila show that this protein binds to HSEs only in heat-shocked cells, suggesting that changes in factor binding are responsible for gene activation. We have investigated the properties of HSE-binding proteins from yeast and HeLa cells. In HeLa cells, binding activity is present only after heat shock. In contrast, control and heat-shocked yeast cells yield the same amount of HSE-binding activity; however, the mobility of protein-HSE complexes on polyacrylamide gels is altered following heat shock. This mobility difference can be significantly reduced by treatment of crude extracts with phosphatase. We propose that the yeast heat-shock factor binds constitutively to DNA but only activates transcription after heat-induced phosphorylation.
TL;DR: More accurate distributions for the side-chain dihedral angles which were obtained from the increased number of proteins determined to high resolution are presented.
TL;DR: Labile tumour-necrosis-factor-like (TNF) activity was detected by means of an enzyme-linked immunosorbent assay in 50% of 226 freshly obtained serum samples from cancer patients with active disease, but the inducing stimulus and the clinical significance of TNF production in cancer are not understood.
TL;DR: It is believed that the concepts of evolutionary homology and sequence or three-dimensional similarity can be kept distinct only if they are referred to with different words.
TL;DR: Gelfand and Serganova as mentioned in this paper considered the Grassmann manifold Gi-, of all (n -k)-dimensional subspaces of C. By fixing the standard basis in C, they obtained an action of the torus H = (,*)I on G[ pk] which is induced from stretching the coordinate axes in C.
TL;DR: Investigation of the convergence properties of this method, in the case of both weighted and unweighted least squares, demonstrates that both give a unique answer and the latter is robust for an homologous family of proteins.
Abstract: An approach is described for modelling the three-dimensional structure of a protein from the tertiary structures of several homologous proteins that have been determined by X-ray analysis. A method is developed for the simultaneous superposition of several protein molecules and for the calculation of an 'average structure' or 'framework'. Investigation of the convergence properties of this method, in the case of both weighted and unweighted least squares, demonstrates that both give a unique answer and the latter is robust for an homologous family of proteins. Multi-dimensional scaling is used to subgroup of the proteins with respect to structural homology. The framework calculated on the basis of the family of homologous proteins, or of an appropriate subgroup, is used to align fragments of the known protein structures of high sequence homology with the unknown. This alignment provides a basis for model building the tertiary structure. Different techniques for using the framework to model the mainchain of various globins and an immunoglobulin domain in the structurally conserved regions are investigated.
TL;DR: It is shown that this sequence activates transcription of a heterologous gene in a cell-cycle-dependent fashion indistinguishable from that of the wild-type HO promoter, which must contain at least two essential upstream activation sequences.
TL;DR: DIF-1, the major bioactive species after purification, has now been identified using a combined microchemical, spectroscopic and synthetic approach and represents a new class of effector molecule.
Abstract: Morphogens are signal molecules presumed to exist in embryos and to be involved in establishing the spatial pattern of cells during development. Differentiation inducing factor (DIF) has the properties of a morphogen required for producing the prestalk/prespore pattern in the aggregate formed by cells of the slime mould Dictyostelium in response to starvation. DIF-1, the major bioactive species after purification, has now been identified using a combined microchemical, spectroscopic and synthetic approach. The structure is defined as 1-(3,5-dichloro-2,6-dihydroxy-4-methoxyphenyl)-1-hexanone, and represents a new class of effector molecule. The availability of relatively large quantities of synthetic and isotopically labelled materials should now allow progress towards a detailed understanding of the pattern-forming processes in Dictyostelium development.
TL;DR: The surface areas of oligomeric proteins, and the areas of the surface buried within them, are directly related to relative molecular mass, which has important implications for the role of subunit interfaces in the stability and activity of oligomers.
Abstract: Protein structures are stabilized by hydrophobic and van der Waals forces, and by hydrogen bonds. The relation between these ther-modynamic quantities and the actual three-dimensional structure of proteins can not be calculated precisely. However, certain empirical relations have been discovered. Hydrophobic energy is gained by the reduction of surface in contact with water1. For monomeric proteins, the area of the surface accessible to solvent, and of that buried in the interior, is a simple function of molecular weight. Proteins with different shapes and secondary structures, but of the same molecular weight, have the same accessible surface area2–5. It has been argued that there is no similar relationship for large oligomeric proteins6. In this paper we show that the surface areas of oligomeric proteins, and the areas of the surface buried within them, are directly related to relative molecular mass. Although oligomers of the same molecular weight bury the same amounts of surface, the proportions buried within and between subunits vary. This has important implications for the role of subunit interfaces in the stability and activity of oligomeric proteins.
TL;DR: It is inferred that microtubules running from the centrosome to the cortex have a central role in aligning the Centrosome-nuclear complex.
Abstract: The establishment of cell division axes was examined in the early embryonic divisions of Caenorhabditis elegans. It has been shown previously that there are two different patterns of cleavage during early embryogenesis. In one set of cells, which undergo predominantly determinative divisions, the division axes are established successively in the same orientation, while division axes in the other set, which divide mainly proliferatively, have an orthogonal pattern of division. We have investigated the establishment of these axes by following the movement of the centrosomes. Centrosome separation follows a reproducible pattern in all cells, and this pattern by itself results in an orthogonal pattern of cleavage. In those cells that divide on the same axis, there is an additional directed rotation of pairs of centrosomes together with the nucleus through well-defined angles. Intact microtubules are required for rotation; rotation is prevented by inhibitors of polymerization and depolymerization of microtubules. We have examined the distribution of microtubules in fixed embryos during rotation. From these and other data we infer that microtubules running from the centrosome to the cortex have a central role in aligning the centrosome-nuclear complex.
TL;DR: A short DNA sequence element, the serum response element (SRE), which binds a nuclear protein, serum response factor (SRF), mediates transient transcriptional activation of c‐fos and cytoskeletal actin genes in response to serum factors.
Abstract: A short DNA sequence element, the serum response element (SRE), which binds a nuclear protein, serum response factor (SRF), mediates transient transcriptional activation of c-fos and cytoskeletal actin genes in response to serum factors. Variant SRE sequences with different affinities for HeLa cell SRF were synthesised. Binding of SRF to these sites in vitro correlates with the transcriptional properties of these elements in vivo, suggesting that SRF is a positively acting transcription factor. A 67-kd polypeptide was identified as the DNA-binding component of SRF by photoactivated DNA-protein cross-linking in vitro. The high affinity SRF-binding site was used to purify this polypeptide to virtual homogeneity in a single DNA affinity chromatography step.
TL;DR: Maternal effect lethal mutations that, on the basis of phenotype and temperature-sensitive period, appear to disrupt this inductive interaction between the early blastomeres in a C. elegans embryo are identified.